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* Academic Reference Workflows and recommendation of Bibdesk
@ 2011-06-03 22:54 Chao LU
  2011-06-04 13:15 ` Matt Lundin
  2011-06-05 15:47 ` Christian Moe
  0 siblings, 2 replies; 4+ messages in thread
From: Chao LU @ 2011-06-03 22:54 UTC (permalink / raw)
  To: emacs-orgmode

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Dear All,

Here I'd like to discuss my workflow for Academic reference and recommend
you Bibdesk.

I use iTune to manage all my mp3 files. Mp3 format has the ability to store
all the metadata into the file itself, and iTune offers a way to modify and
display certain kind of music according to the metadata. Inspired by this, I
was looking for similar way to organize all the academic references and even
to build a personal digital library. I've tried a lot of softwares,
Mendeley, Zotero, Papers, Endnote, Org-mode, Yep, BibDesk...

My feeling is that, Org could get this done, but BibDesk does a better job.
1. The Org-mode Way.*
Learned from this mailing list, I think one of the ways to organize academic
references is like below:

Directory structure:
`--- Library.org
`--- Culture/
`--- Mathematics/
`--- Unix/
`--- .... others

To check in an entry such as "org-manual-7.5.pdf" to the library, one could

#+LINK: pdf file:./Emacs/%s.pdf
#+LINK: txt file:./Emacs/%s.txt

* Emacs
** Org-mode
***  Manual of version 7.5
Location: [[pdf:org-manual-7.5]]
Then use org-attach to get the file settle down in the right place.

To search all the Emacs entries, one could add Library.org to org-agenda
files, then define a related org-agenda command. (It's kind like the smart
group concept in iTune)

However this process is quite time consuming, and non-intuitive. I prefer
the features provided in iTune, Papers2, Bibtex, which could provide
thumbnail and quicklooks of the files.

*2. the Bibdesk way:*
Now I'd like to recommend BibDesk here.

First of all it's free, open resource. Its database file is just an bibtex
file, so all the records is in plain text, even the thumbnails are stored
inside this bibtex file. like below,
Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUIJidUJHRvcFgkb2JqZWN0c1gk....(It's very
long png source code, so I abridged here)}

Second, Bibdesk has a much more intuitive UI, and thumbnails are provided.
It also support keywords, smart groups...

Moreover, Bibdesk has a great feature called autofile, which could attach
the file to certain directories (and build the directories structures you
want as well!) Here is the example:

Again, I want to put our org-manual-7.5.pdf into LibraryRoot/Unix/Emacs/

I just have this Bibtex entry ready:

    Author = {Org-Mode},
    Date-Added = {2011-06-03 16:07:44 -0400},
    Date-Modified = {2011-06-03 16:14:54 -0400},
    Keywords = {/Unix/Emacs,  Emacs},
    Title = {Org-mode Manual},}

Here notice the first keywords is the directory structure I want to have.
Then I set up a template of autofile, (%k[/]1/%l%n0%e), telling BibDesk to
"Build the directory structure based on my first keyword and rename it as
what I want, then check it in".
To me, this workflow for organizing digital references is complete now.

 I do think that BibDesk has great features to investigate, such as create
the record from the bibtex and embed the picture inside the bibtex itself.
Maybe we could also use the *.org as a database file and develop a framework
to have our entries displayed in more intuitive way, maybe by using smart
group, tag(keywords).

Sorry for this such a long post, and looking forward to comments.



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-- links below jump to the message on this page --
2011-06-03 22:54 Academic Reference Workflows and recommendation of Bibdesk Chao LU
2011-06-04 13:15 ` Matt Lundin
2011-06-05 15:47 ` Christian Moe
2011-06-05 16:05   ` Eric Schulte

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